X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/988c59f51aa579ce8bf0eab1cc729e05a5ee5631..9f9cf2e1da7233d6b341602faeaa69454b7e201f:/sdk/cwl/arvados_cwl/pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 27e48f1f44..d083b78f5a 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -8,11 +8,13 @@ import uuid
 import os
 import urllib
 
+from arvados_cwl.util import get_current_container, get_intermediate_collection_info
 import arvados.commands.run
 import arvados.collection
 
 from schema_salad.sourceline import SourceLine
 
+from arvados.errors import ApiError
 from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
 from cwltool.workflow import WorkflowException
 
@@ -42,7 +44,7 @@ class ArvPathMapper(PathMapper):
     pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
 
     def __init__(self, arvrunner, referenced_files, input_basedir,
-                 collection_pattern, file_pattern, name=None, single_collection=False, **kwargs):
+                 collection_pattern, file_pattern, name=None, single_collection=False):
         self.arvrunner = arvrunner
         self.input_basedir = input_basedir
         self.collection_pattern = collection_pattern
@@ -153,9 +155,14 @@ class ArvPathMapper(PathMapper):
                 for l in srcobj.get("listing", []):
                     self.addentry(l, c, ".", remap)
 
-                check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
-                if not check["items"]:
-                    c.save_new(owner_uuid=self.arvrunner.project_uuid)
+                container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+                info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
+
+                c.save_new(name=info["name"],
+                           owner_uuid=self.arvrunner.project_uuid,
+                           ensure_unique_name=True,
+                           trash_at=info["trash_at"],
+                           properties=info["properties"])
 
                 ab = self.collection_pattern % c.portable_data_hash()
                 self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
@@ -167,9 +174,14 @@ class ArvPathMapper(PathMapper):
                                                   num_retries=self.arvrunner.num_retries                                                  )
                 self.addentry(srcobj, c, ".", remap)
 
-                check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
-                if not check["items"]:
-                    c.save_new(owner_uuid=self.arvrunner.project_uuid)
+                container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+                info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
+
+                c.save_new(name=info["name"],
+                           owner_uuid=self.arvrunner.project_uuid,
+                           ensure_unique_name=True,
+                           trash_at=info["trash_at"],
+                           properties=info["properties"])
 
                 ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
                 self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]),
@@ -202,6 +214,7 @@ class ArvPathMapper(PathMapper):
         else:
             return None
 
+
 class StagingPathMapper(PathMapper):
     _follow_dirs = True